Differential gene expression between various tissues and developmental stages can be compared rapidly and efficiently using the RNA arbitrarily primed polymerase chain reaction (RAP) fingerprinting method that was developed in our laboratories. In RAP, a primer of arbitrary sequence primes both first and second strand cDNA synthesis. The mixture of products is PCR amplified and resolved electrophoretically, yielding highly reproducible fingerprints that are tissue-specific. Differences between fingerprints arise from differentially expressed genes. The method samples RNAs with little bias, allowing the identification of novel differentially regulated transcripts. One of the most exciting applications of RAP technology is to brain development. An understanding of spatial and developmental differences in gene expression during development is an important goal in understanding the normal function of the brain and its pathology. The RAP method allows the comparison of many RNA samples simultaneously and, therefore, is capable of detecting among a large sample of expressed genes those few that are expressed for only a brief period during brain development, are expressed in only one or a few areas of the brain, or are differentially expressed between normal brains and those with neurodegenerative disorders. Such genes are attractive candidates for further analysis by conventional strategies. We will identify and characterize such genes from the mouse brain in an international collaborative effort. A pilot study has already demonstrated the feasibility of this approach.